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Dysregulation of bacterial proteolytic machinery by a new class of antibiotics

Nature Medicine volume 11, pages 1082–1087 (2005)Cite this article

A Corrigendum to this article was published on 01 December 2005

Abstract

Here we show that a new class of antibiotics—acyldepsipeptides—has antibacterial activity against Gram-positive bacteria in vitro and in several rodent models of bacterial infection. The acyldepsipeptides are active against isolates that are resistant to antibiotics in clinical application, implying a new target, which we identify as ClpP, the core unit of a major bacterial protease complex. ClpP is usually tightly regulated and strictly requires a member of the family of Clp-ATPases and often further accessory proteins for proteolytic activation. Binding of acyldepsipeptides to ClpP eliminates these safeguards. The acyldepsipeptide-activated ClpP core is capable of proteolytic degradation in the absence of the regulatory Clp-ATPases. Such uncontrolled proteolysis leads to inhibition of bacterial cell division and eventually cell death.

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Figure 1: Structures of ADEPs.
Figure 2: In vivo efficacy of optimized ADEPs.
Figure 3: The target of ADEPs is ClpP.
Figure 4: Effect of ADEPs on peptidase activity and autoproteolytic activity of ClpP.
Figure 5: ADEPs activate the protease function of ClpP.

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Acknowledgements

We acknowledge several scientists at Bayer HealthCare: U. Pleiss for labeling of the ADEP-crosslinker, S. Seip and J. Bennet-Buchholz for determination of the ADEP structure, A. Mayer-Bartschmid and M. Brüning for fermentation of the natural products, B. Wieland for help with purification of native ClpP, E. Sander and I. Loof for pathological analysis of the mice during the toxicology study and G. Schiffer, C. Freiberg, N. Brunner, D. Haebich and K. Ziegelbauer for discussions. We thank T. Msadek (Institute Pasteur, Paris) for strains QB4916 and QB4756, H. Nikaido (University of California, Berkeley) for E. coli HN818 and R. Bartenschlager (University of Heidelberg) for the HUH7 cell line. U. Gerth (University of Greifswald) is acknowledged for providing the His-ClpP producer strain, mutants BUG2 and BUG7, as well as for testing the activity of ADEP 1 against two strains, PS28 and PS46, provided by A.L. Sonenshein (Tufts University, Boston). We are furthermore indebted to T. den Blaauwen and N. Nanninga (University of Amsterdam) and to M. Hecker (University of Greifswald) for discussions. H.-G.S. acknowledges financial support by the Deutsche Forschungsgemeinschaft and the BONFOR program.

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Author notes

  1. Christoph Ladel

    Present address: RBM Serono, Via Ribes1, 10010, Colleretto Giacosa, Italy

  2. Julia E Bandow

    Present address: Pfizer Inc., Global Research and Development, Ann Arbor, Michigan, 48105, USA

  3. Harald Labischinski

    Present address: Combinature Biopharm AG, Robert-Roessle-Str. 10, Berlin, Germany

Authors and Affiliations

  1. Department of Anti-infectives, Bayer HealthCare AG, Pharma Research, Aprather Weg 18a, Wuppertal, D-42096, Germany

    Heike Brötz-Oesterhelt, Dieter Beyer, Hein-Peter Kroll, Rainer Endermann, Christoph Ladel & Harald Labischinski

  2. Enabling Technologies, Bayer HealthCare AG, Pharma Research, Aprather Weg 18a, Wuppertal, D-42096, Germany

    Werner Schroeder

  3. Chemistry, Bayer HealthCare AG, Pharma Research, Aprather Weg 18a, Wuppertal, D-42096, Germany

    Berthold Hinzen, Siegfried Raddatz & Holger Paulsen

  4. Pharmacokinetics, Bayer HealthCare AG, Pharma Research, Aprather Weg 18a, Wuppertal, D-42096, Germany

    Kerstin Henninger

  5. Institute for Microbiology, University of Greifswald, F.-L.-Jahn Strasse 15, Greifswald, D-17487, Germany

    Julia E Bandow

  6. Institute for Medical Microbiology, University of Bonn, Sigmund-Freud-Strasse 25, D-53105, Bonn, Germany

    Hans-Georg Sahl

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Corresponding author

Correspondence to Heike Brötz-Oesterhelt.

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Competing interests

Heike Brötz-Oesterhelt, Dieter Beyer, Hein-Peter Kroll, Rainer Endermann, Christoph Ladel, Werner Schroeder, Berthold Hinzen, Siegfried Raddatz, Holger Paulsen, Kerstin Henninger and Harald Labischinski are employees of Bayer HealthCare AG.

Supplementary information

Supplementary Fig. 1

Nonspecific adsorption of B. subtilis cell lysate (extract out of 0.2 g wet weight) to blank NHS-Sepharose (1 ml column volume). (PDF 58 kb)

Supplementary Fig. 2

Growth of E. coli during overexpression of ClpP from B. subtilis (upper two panels) or its own ClpP (lower two panels). (PDF 92 kb)

Supplementary Fig. 3

Proteome analysis. (PDF 206 kb)

Supplementary Table 1

Effect of ADEPs on eukaryotic cell lines in vitro. (PDF 19 kb)

Supplementary Table 2

Effect of inactivation of all members of the Clp gene family in B. subtilis on the activity of the ADEPs. (PDF 34 kb)

Supplementary Methods (PDF 40 kb)

Supplementary Note (PDF 68 kb)

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Brötz-Oesterhelt, H., Beyer, D., Kroll, HP. et al. Dysregulation of bacterial proteolytic machinery by a new class of antibiotics. Nat Med 11, 1082–1087 (2005). https://doi.org/10.1038/nm1306

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